addtree | R Documentation |
Objects representing additive tree distances.
as.cl_addtree(x)
x |
an R object representing additive tree distances. |
Additive tree distances are object dissimilarities d
satisfying
the so-called additive tree conditions, also known as
four-point conditions d_{ij} + d_{kl} \le \max(d_{ik} +
d_{jl}, d_{il} + d_{jk})
for all quadruples i, j, k, l
.
Equivalently, for each such quadruple, the largest two values of the
sums d_{ij} + d_{kl}
, d_{ik} + d_{jl}
, and d_{il} +
d_{jk}
must be equal.
Centroid distances are additive tree distances where the inequalities
in the four-point conditions are strengthened to equalities (such that
all three sums are equal), and can be represented as d_{ij} = g_i
+ g_j
, i.e., as sums of distances from a “centroid”.
See, e.g., Barthélémy and Guénoche (1991) for more details on additive
tree distances.
as.cl_addtree
is a generic function. Its default method can
handle objects representing ultrametric distances and raw additive
distance matrices. In addition, there is a method for coercing
objects of class "phylo"
from package
ape.
Functions ls_fit_addtree
and
ls_fit_centroid
can be used to find the additive tree
distance or centroid distance minimizing least squares distance
(Euclidean dissimilarity) to a given dissimilarity object.
There is a plot
method for additive tree distances.
An object of class "cl_addtree"
containing the additive
tree distances.
J.-P. Barthélémy and A. Guénoche (1991). Trees and proximity representations. Chichester: John Wiley & Sons. ISBN 0-471-92263-3.
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